X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=scanForPairedEndReads.cpp;h=751fa558833aabce8bac0ae4d02013aae0ac1685;hp=4d1fbfb79ea16d52a0e1b903bd0e40cfc11f66cd;hb=9eef8b58056b7cdaad1b4bdb2b2904d9fc0ff430;hpb=f67ec16ff8add74c17df026f77cf39e5a1aca051

diff --git a/scanForPairedEndReads.cpp b/scanForPairedEndReads.cpp
index 4d1fbfb..751fa55 100644
--- a/scanForPairedEndReads.cpp
+++ b/scanForPairedEndReads.cpp
@@ -10,6 +10,7 @@
 #include "sam/bam.h"
 #include "sam/sam.h"
 
+#include "utils.h"
 #include "my_assert.h"
 
 using namespace std;
@@ -55,7 +56,7 @@ int main(int argc, char* argv[]) {
 	string qname;
 	bool go_on = (samread(in, b) >= 0);
 	bool isPaired;
-	long cnt = 0;
+	HIT_INT_TYPE cnt = 0;
 
 	printf("."); fflush(stdout);